arcs | 🌈Scaffold genome sequence assemblies | Genomics library

 by   bcgsc C++ Version: v1.2.5 License: GPL-3.0

kandi X-RAY | arcs Summary

kandi X-RAY | arcs Summary

arcs is a C++ library typically used in Artificial Intelligence, Genomics applications. arcs has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

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              arcs has a low active ecosystem.
              It has 82 star(s) with 15 fork(s). There are 28 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 1 open issues and 100 have been closed. On average issues are closed in 33 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of arcs is v1.2.5

            kandi-Quality Quality

              arcs has no bugs reported.

            kandi-Security Security

              arcs has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              arcs is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              arcs releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            arcs Key Features

            No Key Features are available at this moment for arcs.

            arcs Examples and Code Snippets

            Function to determine the alignment of an arcs .
            javascriptdot img1Lines of Code : 32dot img1no licencesLicense : No License
            copy iconCopy
            function isAnagram_alt2(s1, s2) {
              if (s1 === s2) {
                return true
              }
            
              if (s1.length !== s2.length) {
                return false
              }
            
              let counter = {}
            
              for (let i = 0; i < s1.length; i++) {
                let charCount = s1.charCodeAt(i)
            
                // Assign this c  

            Community Discussions

            QUESTION

            How to merge DataFrames, combining columns and creating new rows
            Asked 2021-Jun-14 at 14:51

            I have a couple of arcs dataframes with a very similar structure to these:

            Ah: i j 0 1 1 1 1 2 2 2 1 3 2 2 K: Ok Dk 0 3 4 1 1 2 2 2 1

            I need to find a way to create a new dataframe that merges both, following this structure:

            Route: Ok i j Dk 0 3 1 1 4 1 3 1 2 4 2 3 2 1 4 3 3 2 2 4 4 1 1 1 2 5 1 1 2 2 6 1 2 1 2 7 1 2 2 2 8 2 1 1 1 9 2 1 2 1 10 2 2 1 1 11 2 2 2 1

            or this structure:

            Route: i j k 0 1 1 0 1 1 2 0 2 2 1 0 3 2 2 0 4 1 1 1 5 1 2 1 6 2 1 1 7 2 2 1 8 1 1 2 9 1 2 2 10 2 1 2 11 2 2 2

            Currently I have a piece of code that can do something similar to that but instead of a pandas dataframe (which is what I want to use) I'm using dictionaries (the reason behind that is that each "route" has different caracteristics that makes them unique from each other so a dictionary is useful and at the time I was just learning Python) but the issue is that it takes too much time and uses a lot of memory so I'm trying to find a way to make it a little bit quicker, avoiding 'for' loops and trying to apply Pandas to create the merged dataframe.

            This is an extract of the structure of my current piece of code, for this example, consider the 'A' dataframe as the one that holds every combination possible of arcs so the 'if' condition makes sure that a connection exists before creating the route.

            ...

            ANSWER

            Answered 2021-Jun-14 at 14:22

            I think you can use pandas Concat function to merge your dictionaries the way you want to. https://pandas.pydata.org/pandas-docs/stable/user_guide/merging.html

            It's kind of hard to see how you want it to be laid out, but I think you want to use .merge

            Source https://stackoverflow.com/questions/67971916

            QUESTION

            Customize color of lines in Social Network Visual in ggplot2
            Asked 2021-Jun-14 at 07:36

            I'm struggling with the following issue. I visualized a big social network and would like to customize the color palette of the edges captured in geom_segmentfor better visibility. For instance, I want to replace my blue scale by a red scale. How can I achieve that in the easiest way possible?

            I have the following code which is working fine:

            ...

            ANSWER

            Answered 2021-Jun-14 at 07:36

            Thanks to stefan, I used the following code which changed the color from blue to red using scale_color_gradient.

            Source https://stackoverflow.com/questions/67951393

            QUESTION

            Generalized Traveling Salesman Problem in zimpl
            Asked 2021-Jun-14 at 07:17

            I am new to zimpl and I am currently trying to modell the GTSP. The setting is that we have nodes which are grouped into clusters. My problem is i dont know how to implement in zimpl which node belongs to which cluster.

            What I did so far:

            set V:= {1..6}; set A:= { in V*V with i < j};
            set C:= {1,2,3};
            set W:= { in C*C with p < q};
            set P[]:= powerset(C); set K:= indexset(P);

            I am guessing something is missing because i want to group node 1,2 in cluster 1, 3,4 in cluster 2 and 5,6 in cluster 3.

            Some background Information:

            Let G = (V, A) be a graph where V=1,2,...,n is the set of nodes and A = {(i, j): i, j ∈ V, i ≠ j} is the set of directed arcs (or edges), and let c_ij be the travel distance (or cost or time) from node i to node j. Let V1, V2, ... , Vk be disjoint subsets of V such that union of these subsets equals to V. These subsets are called clusters. The GTSP is to find the tour that (i) starts from a node and visits exactly one node from each cluster and turns back to the starting node (ii) never visit a node more than once and (iii) has the minimum total tour length. Associated with each arc, let x_ij be a binary variable equal to “1” if the traveler goes from node i to node j, and “0” otherwise.

            Thats the mathematicl model I want to model: min∑i∈V ∑j∈V\{i} cijxij subject to: ∑i∈Vp ∑j∈V\Vp xij = 1 (p= 1, ..., k) ∑i∈V\Vp ∑j∈Vp xij = 1 (p= 1, ..., k) ∑j∈V\{i} xji − ∑j∈V\{i} xij = 0 (∀i∈V) xij∈{0,1} ∀(i, j)A up−uq+k ∑i∈Vp ∑j∈Vq xij+(k−2)∑i∈Vq ∑j∈Vp xij ≤ k−1 (p≠q;p,q=2,...,k) up≥0 (p=2, ..., k) (Thats the link for the paper: http://www.wseas.us/e-library/conferences/2012/Vouliagmeni/MMAS/MMAS-09.pdf)

            Maybe someone can help! thanks

            ...

            ANSWER

            Answered 2021-Jun-12 at 15:36

            You can use an indexed set (just as u did to implement the powerset of C) and assign the sets as needed. Try this for example:

            Source https://stackoverflow.com/questions/67919056

            QUESTION

            How to create Inner rounded Box Flutter
            Asked 2021-Jun-12 at 20:19

            How can I make a Box like this the easiest way?

            I tried a lot with CustomPainter and Arcs or CustomClippers but failed. I know its possible with those techniques but I could not manage to do it. (Please include the code if possible I lost way too much time on this already)

            ...

            ANSWER

            Answered 2021-Jun-12 at 20:19
            class MyApp extends StatelessWidget {
            @override
            Widget build(BuildContext context) {
               return MaterialApp(
               title: 'Drawing Paths',
               home: Container(
                 color: Colors.white,
                 child: CustomPaint(
                   painter: CurvePainter(),
                  ),
                 ),
                );
               }
              }
            
            class CurvePainter extends CustomPainter {
            @override
            void paint(Canvas canvas, Size size) {
            var paint = Paint();
            paint.color = Colors.green[800];
            paint.style = PaintingStyle.fill; // Change this to fill
            
            Path path = Path();
            path.moveTo(0, size.height * 0.5);
            path.quadraticBezierTo(0, size.height * 0.2, 0, size.height * 0.1);
            path.lineTo(size.width, size.height * 0.1);
            path.lineTo(size.width, size.height * 0.5);
            path.quadraticBezierTo(
                size.width * 0.5, size.height * 0.25, 0, size.height * 0.5);
            path.close();
            
            canvas.drawPath(path, paint);
            }
            
             @override
             bool shouldRepaint(CustomPainter oldDelegate) {
            return true;
            }
            }
            

            Source https://stackoverflow.com/questions/67952218

            QUESTION

            How to calculate the area of two circles' intersection?
            Asked 2021-May-28 at 04:06

            The topic link: https://codeforces.com/problemset/problem/600/D

            For the question, I'm wrong answer on test28, which could look like this:

            correct answer:119256.95877838134765625000

            my answer: 120502.639190673828125

            I guess it is caused by calculation accuracy, but I don't have evidence. Maybe algorithm itself is faulty, please point it out.

            Algorithm ideas:

            For any given two circles, in order to simplify the calculation, we can translate the origin of the coordinates to the center of one of the circles, and then rotate the other circle to the x-axis by rotating. For calculating the intersection area of the circles, before and after are equivalent, and finally a purple circle and a red circle are formed. In fact, the final intersection area is equal to the sum of the areas of the two sectors minus the area of the diamond in the middle(the figure below, Horizontal axis x, vertical axis y). However, before that, we must first calculate the intersection point of the two circles.

            The coordinates of the center of the first circle at the beginning: .

            The coordinates of the center of the second circle at the beginning: .

            The coordinates of the center of the first circle after a series of transformations: .

            The coordinates of the center of the second circle after a series of transformations: ,

            .

            The equations of two circles are combined:

            are the radius of the first and second circles respectively,so:

            we can use the sector area formula : ,

            , .

            In this place, there will be problems with the positive and negative values of the radian(the two figures below), but it can be proved that they can be absorbed in the final result.

            The final result is the sum of the areas of the two arcs minus the area of the middle diamond.

            mycode:

            ...

            ANSWER

            Answered 2021-May-27 at 06:10

            Don't use too many intermediate floating variables to get to the final answer. Small inaccuracies when add up lead to huge inaccuracy which you can clearly see in the expected and real output in your question. What you can do is to minimize these intermediate floating variables. For example

            Source https://stackoverflow.com/questions/67715025

            QUESTION

            Data binding in d3 v3 donut chart
            Asked 2021-May-23 at 16:46

            So I've been trying to create a donut chart in d3.js and am having trouble adding labels to the chart. My chart data is in an array, but I think because of the "pie" variable, only the "value" from the data is being passed through and not the "text". Have tried multiple ways to try and bring the "text" in but with no luck. Hopefully a fresh set of eyes can see where my mistake is!

            ...

            ANSWER

            Answered 2021-May-23 at 16:46

            Here is how you can add labels:

            Source https://stackoverflow.com/questions/67661298

            QUESTION

            Boost Graph max-flow algorithm to find out the arcs on the minimal S/T cut
            Asked 2021-May-20 at 15:00

            I have an application where for a given fixed number of vertices, there is a need to solve large number of different max-flow algorithms from a given fixed source (S) to a given fixed sink (T). Each max-flow problem differs in that the directed arcs themselves change along with their capacities. As an example, see below.

            The number of vertices remains fixed, but the actual arcs and their capacities differ from one problem to the next.

            I have the following code that solves the max-flow problem iteratively for Graph 1 and Graph 2 in the figure above using boost thus (apologies for the wall of text, I have tried to make it as minimal as possible. The code below fully compiles on g++ on my linux box, but I am unable to have this correcly compile on online compilers such as wandbox, etc.):

            ...

            ANSWER

            Answered 2021-May-20 at 15:00

            There's many issues. If you use modern C++ and compiler warnings, you can reduce the code and spot the bugs in printing vertex descriptors (printf is just not safe; use the diagnostics!).

            Here's my take after review.

            Notable changes:

            • bundled properties instead of separate interior properties

            • this implies passing named arguments (but see https://stackoverflow.com/a/64744086/85371)

            • no more global variables, no more loopy initialization if the simple constructor suffices

            • no more duplicated code (nothing invites error quite like having capacities1 and capacities2 lying around)

            • using clear_vertex instead of just clear_out_edges - this may not make a difference (?) but seems to express intent a bit better

            • no more printf (I'll use libfmt, which is also in c++23), so e.g.

            Source https://stackoverflow.com/questions/67617469

            QUESTION

            D3.js pie chart not showing all arcs
            Asked 2021-May-12 at 11:50

            I have started to learn d3.js. My main goal is zoomable sunburst chart but trying to learn whole library and using it I am trying to create a pie chart. In the pie chart all the arcs are not showing. Please guide regarding this.

            CSS:

            ...

            ANSWER

            Answered 2021-May-12 at 11:50

            Fixed some minor bugs and removed the try/catch block, see it's working in the fiddle:

            Source https://stackoverflow.com/questions/67497513

            QUESTION

            How to determine if a Point is inside of a 2D Polygon that has Arcs
            Asked 2021-May-11 at 15:04

            I have been using the following references to try to determine if a Point is inside of a 2D Polygon that has Arcs:

            Is a point inside of 2D polygon, no curves

            Is a point inside a compound polygon (C#)

            Is a point inside a curve (Theory)

            My approach uses Ray Casting to determine if a point is within the polygon boundary. This is my code that attempts to string the references together (C#):

            ...

            ANSWER

            Answered 2021-May-10 at 15:55

            I asked this question in the AutoDesk .NET Forum and recieved this solution: The Answer

            Source https://stackoverflow.com/questions/67472380

            QUESTION

            Restricting a point to an arc on a circle's circumference
            Asked 2021-May-09 at 16:04

            This question is a bit specific. Assume for simplicity that I have a unit circle, i.e. a circle centered on the origin (0,0) with radius 1. On this circle I have three points: A, B, and C. Assume that B and C are fixed, and that A can be moved along the circle's circumference.

            Question: What conditions can I check efficiently to ensure that A is not moved outside the arc between B and C originally containing it?

            As a point of clarification: I do not just wish to detect whether the point is on this arc or not (i.e., get a boolean), but to have a quantifiable measure (for example, of distance) so I can prevent it from being moved outside. You can imagine my setup like this, restricting point A to the red arc:

            Here are some ideas I have pondered so far, but none were successful:

            • Limit the angle alpha of A = [cos(alpha),sin(alpha)] to the origin between the angles beta and gamma of B=[cos(beta),sin(beta)] and C=[cos(gamma),sin(gamma)], where alpha, beta, and gamma are angles in radians. Unfortunately, this naive case only works in scenario (a) above. If the arc to which A is restricted crosses the (in my case, western) discontinuity from +pi/-pi, a naive upper and lower bound won't do.
            • Calculate the length of the arcs between A-to-B and A-to-C, then ensure that as A is moved this sum does not change. Unfortunately, I have only found this solution to calculate the arcs between two points, and it always calculates the shorter arc. In scenario (c), however, the correct arc A-to-B is the larger one.
            ...

            ANSWER

            Answered 2021-May-08 at 22:22

            Given any two points on a circle, in your case B and C, there are of course two possible arcs. We use A to select between the two options. You say you want to prevent a point, say D, from moving outside this arc. I'm interpreting this to mean that we want a function which, if D lies on the arc defined by BC and A, returns D, otherwise it returns B or C, depending on which is nearer to D.

            We can define the following function to implement this scheme:

            Source https://stackoverflow.com/questions/67452264

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install arcs

            You can download it from GitHub.

            Support

            The ARCS+LINKS pipeline requires two input files:. The Makefile located here: bin/arcs-make will run the full ARCS pipeline. It will also optionally run the misassembly corrector Tigmint prior to scaffolding with ARCS.
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